You have identified the ineptness of Obama and Clinton. An ineptness based on false premises as to the intentions of a large sector of the Muslim world.
Whether or not Islam is a "religion of peace" is a subject for theologians. But, it is evident that certain groups within it feed on certain chapters of the Koran to incite hatred for the non-Muslim world.
The threat to western civilization is real and must be intelligently (and forcefully) addressed.
The Obama administration appears to be blind to this reality.